[Chimera-users] HBond on every frames of a large trajectory

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 22 14:41:15 PDT 2016


Hi Jérémie,
I suspect the problems may be due to the large data size rather than using the hbonds command in per-frame scripting.  It is common to combine hbonds with per-frame scripting of trajectories... it’s even in a tutorial:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1>

However, if you had a specific example of what you mean by not working, and the problem is reproducible (say on a smaller dataset that you could easily share with us), you could use menu: Help… Report a Bug.

I’ll have to leave it to others with no-GUI scripting experience to say whether there is a way to get these results without displaying the trajectory frames.
Sorry about the difficulties,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 22, 2016, at 9:30 AM, Jérémie KNOOPS [531802] <Jeremie.KNOOPS at umons.ac.be> wrote:

> Hi,
> 
> What is the easiest and fastest way to get the number of H bonds on every frame of a large trajectory (>10 000 frames) and print it to a file? 
> The hbonds command does not seem to work with the perframe command and displaying the whole trajectory to run a per-frame script is quite slow.
>  
> Jérémie Knoops
> PhD Student




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